The 30 environmentalists have been held on piracy charges since trying to scale the Prirazlomnaya oil rig on Sept. 18.
“The Chancellor expressed her concern to Putin over the arrest of the crew of the Greenpeace boat, impounded in Russia, and voiced her hope that this case will soon be resolved,” Merkel’s spokesman said in a statement.
Germany has become an increasingly vocal critic of Moscow’s record on human rights, despite Russia’s importance as an energy exporter, straining personal ties between Merkel and Putin.
A Kremlin statement about the leaders’ telephone call made no mention of the activists.
The Greenpeace members, who come from nearly 20 countries, have been ordered held until late November pending further investigation.
Courts have denied bail to a number of them in the past week, including the American captain of the Arctic Sunrise.
On Wednesday, judges in the northern Russian city of Murmansk denied bail to four more people – Anthony Perrett of Britain, Gizem Akhan of Turkey, Jonathan Beauchamp of New Zealand and Francesco Pisanu of France.
The piracy charges, punishable by up to 15 years’ jail, appear aimed at sending a message that Moscow will not tolerate attempts to disrupt its development of the resource-rich Arctic.
Greenpeace says the protest at the rig, owned by state-controlled Russian energy company Gazprom, was peaceful and calls the piracy charges absurd and unfounded.
Putin has said the activists were not pirates but that they had violated international law. The head of the Kremlin’s human rights advisory body has said he would ask prosecutors to withdraw the piracy charges.
Investigators have also said more charges will be pressed against some protesters as drugs and other suspect items had been found on the ship.
Greenpeace denies there were any illegal items aboard.
(Reporting by Alexandra Hudson in Berlin and Alexei Anishchuk in Moscow, editing by Gareth Jones)
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